Flatheads is a term used by the the Others (Cro Magnon) to describe members of the Clan (Neanderthals). It refers to one of the most defining features of Neanderthals - their skulls, which are relatively flat and non-protruding the way Cro Magnons are. Over time, the term flathead has become derogatory, and is used as a slur against the Clan (and as an insult towards Cro Magnon, especially those who are half-Clan).
The term 'flathead' is first used in The Valley of Horses. It is commonly used by the Zelandonii and Mamutoi, though some people stop using it and call Neanderthals 'Clan' instead, due to opposition from Ayla, who finds the term's xenophobic connotations understandably offensive.